Subject: Fwd: CCL:The pi-pi stacking of hetero-aromatic ring

From: arashid=at=iqe.phys.ethz.ch
Date: Sun, 23 May 2004 22:19:44 +0000

Forwarded Message:
> To: Arvydas Tamulis <tamulis=at=mserv.itpa.lt>
> From: Per-Ola Norrby <pon=at=kemi.dtu.dk>
> Subject: CCL:The pi-pi stacking of hetero-aromatic ring
> Date: Fri, 21 May 2004 19:09:08 +0200
> -----
<pre>
>Would you please to advise us the quantum chemical methods and programs
>that might properly calculate stacking interactions including
>dispersion effects in oligomeric nucleic acids (two types of interactions:
>in parallel planes and when planes are perpendicular).

	I don't think there is any QM method able to treat oligomeric 
nucleic acids which can also include accurate dispersion.  DFT or HF 
do NOT include dispersion.  The lowest level I know which does 
include some of the dispersion is MP2, and with any feasible basis 
set for this large system, the basis set deficiency error would be 
expected to totally swamp the dispersion.  The same would be true for 
any correlated method.  (I'll probably be flamed for this statement, 
but I believe it; I don't have proof though, so don't ask for it). 
Counterpoise correction might bring the error down, but certainly not 
to zero.

	You can get the dispersion term accurately from empirical 
force fields.  This is a very well known term, and it has been 
accurately parameterized for many years.  With many force fields, you 
will treat other non-bonded terms erroneously (like in any method 
that uses Lennard-Jones, where the repulsion is strongly 
overestimated), and the electrostatics are always a problem.  I saw a 
JCC article a few years ago which augmented DFT with an empirical 
dispersion term (I don't have the reference), that seems a feasible 
approach.  Otherwise, I'd take a force field that has proven to treat 
DNA well, like AMBER, it's probably superior in quality to any 
achievable QM.  And of course it's several orders of magnitude 
faster...  Not that I use it myself, I'm an MM3 fan, but I wouldn't 
advocate MM3 for oligonucleotides unless you take the electrostatics 
> from a QM source.

	Note that in DFT and HF, you always see an attractive force 
at something similar to the vdW distance.  It's not dispersion, it's 
a simple basis set superposition error together with any 
electrostatic attraction your complex might have.  Sometimes it has a 
similar value to the dispersion, but I wouldn't trust the predictive 
value of this error cancellation.

	If you absolutely have to have your dispersion from QM, you 
could probably set up some kind of extrapolation scheme, like IMOMO 
or ONIOM, where you use CCSD(T) with a large basis for a very small 
core.  It will only give you accurate dispersion for a small 
subsystem though.  You can always validate your final result by 
comparing to a good empirical force field...

	/Per-Ola
-- 
Per-Ola Norrby, Assoc. Professor, <a 
href="http://organisk.kemi.dtu.dk/PON/">http://organisk.kemi.dtu.dk/PON/</a>
Technical University of Denmark, Department of Chemistry
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: pon=at=kemi.dtu.dk  tel +45-45252123,  fax +45-45933968

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